Method for selecting patient specific therapy

Abstract

Methods of identifying a druggable target in a subject suffering from cancer comprising determining at least one unbalanced process in the subject's expression data and selecting at least one gene and/or protein from the at least one unbalanced process wherein a drug that targets that gene or protein is known.

1 . A method of identifying a druggable target, in a subject suffering from cancer, the method comprising,
 a. receiving expression data from said subject;   b. adding said subject's expression data to a first composite cancer-expression data set to produce a second composite cancer-expression data set;   c. determining within said second composite cancer-expression data set at least one unbalanced process, wherein said determining comprises performing thermodynamic-based analysis;   d. identifying within said subject's expression data at least one of said at least one unbalanced processes within said second composite cancer-expression data set; and   e. selecting at least one gene and/or protein from said at least one unbalanced process within said subject's expression data for which a drug that targets said gene or protein is known;   
       thereby identifying a druggable target in a subject suffering from cancer. 
     
     
         2 . The method of  claim 1 , wherein said expression data is protein expression data or mRNA expression data. 
     
     
         3 . The method of  claim 1 , wherein said receiving expression data comprises receiving a biological sample from said subject and performing high-throughput sequencing on said sample. 
     
     
         4 . The method of  claim 3 , wherein said biological sample is a blood sample or a tumor biopsy. 
     
     
         5 . The method of  claim 1 , further comprising normalizing said subject's expression data with a composite healthy-expression data set or with a composite healthy and cancer-expression data set. 
     
     
         6 . The method of  claim 1 , wherein determining at least one unbalanced process comprises determining over and under expressed genes and/or proteins as compared to their expression in a balanced process. 
     
     
         7 . The method of  claim 1 , wherein determining at least one unbalanced process comprises assembling expressed genes and/or proteins within said second data set into networks. 
     
     
         8 . The method of  claim 7 , wherein said assembling is performed using functional interactions according to the STRING database. 
     
     
         9 . The method of  claim 1 , wherein said thermodynamic-based analysis comprises surprisal analysis. 
     
     
         10 . The method of  claim 1 , wherein said first composite cancer-expression data set comprises data from at least 1 type of cancer. 
     
     
         11 . The method of  claim 10 , wherein said different types of cancer are selected from lymphoma, bladder cancer, gastric cancer, colorectal cancer, kidney cancer, ovarian cancer, endometrial cancer, lung cancer, head and neck cancer, brain cancer and breast cancer. 
     
     
         12 . The method of  claim 1 , wherein said first composite cancer-expression data set comprises data from at least 10 samples. 
     
     
         13 . The method of  claim 1 , wherein said selected at least one unbalanced process is selected from Table 1. 
     
     
         14 . The method of  claim 1 , wherein said at least one gene or protein is over or under expressed in said subject's expression data. 
     
     
         15 . The method of  claim 1 , wherein said at least one gene or protein is a known cancer regulatory gene or protein. 
     
     
         16 . The method of  claim 1 , wherein said at least one gene or protein is selected from Table 1 and Table 3. 
     
     
         17 . The method of  claim 1 , further comprising administering to said subject said known drug. 
     
     
         18 . A method for patient-specific cancer treatment, the method comprising,
 a. identifying at least one druggable target specific to said patient using the method of  claim 1 ; and   b. administering to said subject at least one drug that targets said at least one druggable target,   
       thereby providing patient-specific cancer treatment. 
     
     
         19 . The method of  claim 18 , further comprising repeating the method of  claim 1  after a period of treatment with said at least one drug to determine at least one new druggable target. 
     
     
         20 . (canceled) 
     
     
         21 . (canceled) 
     
     
         22 . A computer program product for identifying a druggable target, in a subject suffering from cancer, comprising a non-transitory computer-readable storage medium having program code embodied thereon, the program code executable by at least one hardware processor to
 c. receive expression data from said subject;   d. add said subject's expression data to a first composite cancer-expression data set to produce a second composite cancer-expression data set;   e. determine within said second composite cancer-expression data set at least one unbalanced processes, wherein said determining comprises performing thermodynamic-based analysis;   f. identify within said subject's expression data at least one of said at least one unbalanced processes within said second composite cancer-expression data set; and   g. provide an output of at least one gene and/or protein from said at least one unbalanced process within said subject's expression data for which a drug that targets said gene or protein is known.